I assume you mean the OSGi Framework run configuration that comes standard with the eClipse Plugin development environment and not the one that comes with bndtools.
In that case, the bundles shown in the launcher depend on the definition of the Target platform. This platform is a set of bundles that are added to your plug-in projects for the run configuration. The default definition is the eClipse runtime.
You can define your own target platform via New...Target Definition option in the Plugin development view. In this target definition you can add some directories, features or eClipse plugins that you want to include, which allows you to add your own directory with bundles. Afterwards you can define this target as the target definition to use for the workspace by pressing the link "Set as target platform" in the Target definition edit window.